Expression data from egy wildtype and mutant embryo comparison. Danio rerio

U4/U6 di-snRNPs were disrupted and singular U4 and U6 snRNPs accumulated in egy mutant embryos, establishing the recycling function of p110 in vivo. Based on microarray analyses, a subset of spliceosome components and splicing-related factors was coordinately upregulated in the egy mutant. This revealed an extensive network of coregulated components of the spliceosome cycle, compensating – albeit inefficiently – for the recycling defect. In contrast, another set of genes, many of them eye- and pancreas-specific, was downregulated in the egy mutant embryos. Keywords: mut / wt comparison Overall design: Zebrafish earl grey (egy) mutant embryos carry an autosomal recessive defect in the p110-orthologous gene which leads to microcephaly, microphthalmia, underdevelopment of the pharyngeal arches, and thymus hypoplasia by day 8 of development. To characterize the defect on the transcriptional level, egy whole embryos (n>100) were collected and morphologically separated into pools of mutant (mut) and wildtype (wt) sibling embryos. Pools of embryos were collected at 2 time points (3 and 4 days post fertilization) with 2 and 3 biological replicates, resp.. After RNA extraction, labelled cRNA was hybridized onto Affymetrix microarrays.

U4/U6 双小核核糖核蛋白颗粒（U4/U6 di-snRNPs）在egy突变体胚胎中发生解离，游离的U4与U6小核核糖核蛋白颗粒（small nuclear ribonucleoprotein particles, snRNPs）出现异常积累，由此证实了p110在体内的循环回收功能。
通过微阵列芯片（microarray）分析发现，egy突变体中一组剪接体（spliceosome）组分与剪接相关因子发生协同上调。这揭示了剪接体循环中一系列协同调控组分所构成的广泛调控网络，尽管代偿效率有限，但可对该循环回收缺陷起到补偿作用。
与之相反，另一组基因（其中多数为眼组织与胰腺组织特异性基因）在egy突变体胚胎中出现表达下调。

关键词：mut/wt 对照
实验设计概述：
斑马鱼灰耳（egy）突变体胚胎携带p110同源基因的常染色体隐性缺陷，该缺陷会导致胚胎发育至第8天时出现小头畸形、小眼畸形、鳃弓发育不全以及胸腺发育不良。
为从转录层面表征该缺陷，研究人员收集了超过100枚整胚，并通过形态学特征将其分为突变体（mut）与野生型（wt）同窝胚胎两组。实验分别在受精后3天与4天两个时间点收集样本，各时间点对应的生物学重复数分别为2次与3次。完成RNA提取后，将标记好的互补RNA（cRNA）与Affymetrix微阵列芯片进行杂交。